Introduction to Cytoscape and it’s Apps - Session 1 B

Part B: Public Repositories

Pathway data

• WikiPathways
• Reactome
• KEGG
• Pathway Commons (collection)
• Published Pathway Figures

Network data

• STRING
• IntAct
• NDEx (collection)

Sources of PPI Data

• Experimental Techniques High Throughput Low Throughput
• Computational Techniques
• Public Repositories

Know what to look for. Know what you’re getting.

Finding Network Data

Where do I find the network?

• There is no such thing!

• There are hundreds of different interaction databases

• It depends on your biological question and your analysis plan,

But know what you are getting…..

Starting with a gene list……

Networks

Broad coverage / Lower resolution

• STRING (stringApp)
• NDEx (built-in)
• PSICQUIC (built-in)
• IntAct (IntAct App)

String

StringApp

Use the Network Search Tool to select a resource:

STRING Settings

STRING Results

STRING Options

STRING Enrichment

NDEx

CyNDEx App

• Repository for biological network knowledge
• Organisations and individual scientists can deposit
• Use CyNDEx App to import/export networks
• Featured collections include:
  • Pathway Interaction Database (NCI-PID)
  • Cancer Cell Maps Initiative (CCMI)
  • The NDEx Butler
  • NetPath

PSICQUIC

PSI common query interface

PSICQUIC is included in the Cytoscape network search tool:

IntAct

IntAct App

IntAct - Filters

• Can filter network by:
  • MI Score
  • Interaction detection method
  • Participant detection method
  • Host organism
  • Expansion (e.g. spoke vs. matrix)
  • Type (interaction type)
  • Mutations (hides unmutated edges)

Pathways

Higher resolution / Limited coverage (~50% of genes)

• WikiPathways (WikiPathways App)
• Reactome (ReactomeFI App)
• Pathway Commons (CyPath2 App)
• KEGG (KEGGscape App)

WikiPathways

WikiPathways App

• Handmade pathway models
• Collaborative platform open to all researchers
• Thousands of pathways for dozens of species

Use the Network Search Tool to select a resource:

WikiPathways Search

WikiPathways Results

Pathway Database Apps

Cytoscape

Core Concepts

Cytoscape Apps!

apps.cytoscape.org

Loading Network Data

Cytoscape can import network data from:

• Files (or URLs)
  • Excel, TSV, CSV
  • XGMML: eXtensible Graph Markup and Modelling Language
  • SBML: Systems Biology Markup Language
  • BioPAX
  • PSI-MI
  • SIF: Simple Interaction Format
  • GML: Graph Markup Language
  • … and others depending on loaded Apps

Cytoscape can import network data from:

• Public repositories:
  • PSICQUIC
  • STRING (via the stringApp)
  • IntAct (via the IntActApp)
  • Reactome (via the ReactomeFI app)
  • WikiPathways (via the WikiPathways app)
  • Pathway Commons (via the CyPath2 app)
  • NDEx
• Automation:
  • Command line scripts
  • CyREST via R, Python, etc

Cytoscape can load tables from:

• Files (or URLs)
  • Excel, TSV, CSV
• Public repositories
  • BioMart
• Automation:
  • Command line scripts
  • CyREST via R, Python, etc

Saving and Exporting

• Sessions save everything as .cys files: Networks, Tables, Styles, Screen sizes, etc.
• Export networks in different formats: SIF, GML, XGMML, BioPAX, JSON
• Export tables as CSV files
• Publication quality graphics in several formats: PDF, SVG, PNG, and JPEG

Tour of Cytoscape - Exercise

• Launch the latest version of Cytoscape

* Save your cytoscape app as a session in .cys format for future use.